Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
نویسندگان
چکیده
منابع مشابه
RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
MOTIVATION To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. RESULTS Here we p...
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A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented. The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically corr...
متن کاملFitting atomic models into electron-microscopy maps.
Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 A resolution can produce structural information that is accurate to about 2.2 A resolution. In an initial step, it is necessary to determine accurately the absolute scale and absolute hand of the cryo-electron microscopy map, the...
متن کاملFitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.
Recent experimental advances in producing density maps from cryo-electron microscopy (cryo-EM) have challenged theorists to develop improved techniques to provide structural models that are consistent with the data and that preserve all the local stereochemistry associated with the biomolecule. We develop a new technique that maintains the local geometry and chemistry at each stage of the fitti...
متن کاملAccurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.
Cryo-electron microscopy (cryo-EM) has been widely used to explore conformational states of large biomolecular assemblies. The detailed interpretation of cryo-EM data requires the flexible fitting of a known high-resolution protein structure into a low-resolution cryo-EM map. To this end, we have developed what we believe is a new method based on a two-bead-per-residue protein representation, a...
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ژورنال
عنوان ژورنال: IUCrJ
سال: 2019
ISSN: 2052-2525
DOI: 10.1107/s2052252519007619